schrodinger.application.matsci.pbcutils module¶
Utility functions and classes for pbcs
Copyright Schrodinger, LLC. All rights reserved.
- schrodinger.application.matsci.pbcutils.get_disorder_groups(struct)¶
Get atoms that have s_cif_disorder_group set and occupancies are not 0 or 1.
- Parameters
structure.Structure – Input structure
- Return type
dict or None
- Returns
Dict with keys disorder group labels, values list of atom indices or None if nothing is present in the structure
- schrodinger.application.matsci.pbcutils.remove_pbc_props(struct)¶
Remove the pbc properties of the given structure.
- Parameters
struct (schrodinger.structure.Structure) – crystal structure from which all the pbc properties are to be removed
- schrodinger.application.matsci.pbcutils.translate_to_hb_cell(pos, vecs)¶
Translate atoms to the cell around origin (between -0.5 and 0.5) using copied input structure.
- Parameters
pos (numpy.array) – List of atomic positions
vecs (numpy.array) – List of lattice vectors
- Return type
numpy.array
- Returns
Updated atomic positions
- schrodinger.application.matsci.pbcutils.get_nearest_image(reference_pos, pos, pbc)¶
Get the nearest image of the passed positional coordinates to reference_pos using pbc
- Parameters
reference_pos (list) – The reference position
pos (list) – The position to get the nearest image of
pbc (
schrodinger.structutils.pbc.PBC) – The PBC object for the structure
- Return type
tuple
- Returns
The nearest image position to the reference